Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are
restrained runs to remove/dampen clashes and prevent crashes but if you are
already running a full md simulation then you don't need to redo those steps.
Also, I don't use DispCorr for C36 lipids (some debates about that can b
Today I've performed test simulation of the protein-cAMP complex with
the charmm27 force field and obtain good stable system. I've compared
polar contacts of my complex ( ligand have been done with SwissParam)
with the X-ray structure of that protein solved with the same complex
and obtained simila
On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
> 1- on what assumptions that blocks were generated ?
This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it
This is fixed in 4.6-beta1, though I am using the mpi version instead of the
single-node threaded version.
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Hi,
I have been trying to rigorously check my .itp (topology) files for errors.
Is it true that .itp files allow scientific notation?
For example, suppose that I want to specify sigma = 0.35 nm in
ffnonbonded.itp. If I enter either
3.5e-1
or
3.5E-1
will these entries indeed specify
On 12/8/12 12:53 PM, Andrew DeYoung wrote:
Hi,
I have been trying to rigorously check my .itp (topology) files for errors.
Is it true that .itp files allow scientific notation?
For example, suppose that I want to specify sigma = 0.35 nm in
ffnonbonded.itp. If I enter either
3.5e-1
or
Hi,
I am sure that this is a rather basic question, but I am wondering if you
can please help me to understand something described in the manual.
What is the purpose of the [ pairs ] section of an .itp file? What
information does it contain?
Section 5.3.4 (page 112) of the version 4.5.4 manua
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